CodeFusion

CodeFusion is a tool that helps coding diagnoses and medical phrases using ICD or other WHOFIC classifications. In addition, it has features for creating mapping suggestions between WHOFIC and other terminologies.

The tool can read Excel (.xlsx) and tab-separated text files (.txt) and matches the text found in these files to codes and URIs

It can be used in Web UI mode or as a command-line tool. In Web UI mode, run the tool with --ui (or use the platform launcher scripts) as described in the User Guide. In command-line mode, you can run it from a terminal window using parameters explained below. Alternatively, you can provide the parameters in a file named parameters.json in the same folder as the executable. A sample parameters.json file is provided together with the executable.

IMPORTANT! It is recommended to have the automated coding reviewed by a human coder especially when the matching level is not GoodMatch (see MatchLevel in the Output File section).

Downloading and Installation

The most recent version of the tool is version:1.1.2.

The tool can be downloaded from the following links. Please use the operating system and architecture that matches your computer.

Platform Installer
Windows x64 CodeFusion_win-x64_1.1.2.msi CodeFusion_win-x64_1.1.2.zip
Windows Arm64 CodeFusion_win-arm64_1.1.2.msi CodeFusion_win-arm64_1.1.2.zip
MacOS Apple Silicon (M1 and later) codefusion_osx-arm64_1.1.2.tar.gz
MacOS Intel codefusion_osx-x64_1.1.2.tar.gz
Linux x64 codefusion_linux-x64_1.1.2.tar.gz
Linux Arm64 codefusion_linux-arm64_1.1.2.tar.gz

Windows Installation

The easiest way is to download the installer (.msi) and run it. It installs CodeFusion for your user account (no administrator rights needed), adds a CodeFusion shortcut to the Start menu (and optionally to the desktop) that starts the Web UI, and creates the CodeFusionFiles folder in your Documents folder which is the folder that you use to save the files you'd like to process with CodeFusion

The installer also adds the installation folder (%LocalAppData%\Programs\CodeFusion) to your PATH, so you can run CodeFusion from any new terminal window.

Updating: run the installer of the new version; the old version is replaced automatically. Every version installs its own default parameters.json, because settings of an older version may not be compatible with the new one. If you had changed parameters.json, your old file is kept in the installation folder as parameters_<date>_<time>.json (for example parameters_2026-10-28_112738.json), so you can copy your settings over to the new file if they still apply.

Alternatively, download the zip file and unzip it to a folder.

macOS Installation

CodeFusion for macOS comes as a single app, CodeFusion.app, which contains everything it needs. Download the package that matches your Mac: Apple Silicon for Macs with an M1 or later chip, Intel for older Macs. To check, open the Apple menu > About This Mac: it shows Chip: Apple M… on Apple Silicon Macs and Processor: … Intel … on Intel Macs.

  1. Extract the downloaded tar.gz file
    Double‑click it in Finder. This creates a folder named codefusion_osx-arm64_1.1.2 (Apple Silicon) or codefusion_osx-x64_1.1.2 (Intel) containing CodeFusion.app.

  2. Move CodeFusion.app to your Applications folder
    Drag it to Applications (or to Applications in your home folder if you are not allowed to change the main one).
    Do not run CodeFusion from a USB drive, a network share or the Downloads folder: macOS blocks apps started from Finder from reading files in those places, and CodeFusion will not start.

  3. Remove the quarantine flag
    CodeFusion is not distributed through the App Store, so macOS blocks it until you remove the quarantine flag. Open Terminal and run:
    xattr -cr /Applications/CodeFusion.app

  4. Start CodeFusion
    Double‑click CodeFusion.app. The Web UI opens in your browser and shows the CodeFusionFiles folder where you put the files to process (click the ? button next to the folder name for details). If macOS asks whether CodeFusion may access a folder, choose Allow. CodeFusion stops automatically when you close the Web UI.

Running CodeFusion from the Terminal on macOS

The CodeFusion program is inside the app and can be run with its full path, for example:
/Applications/CodeFusion.app/Contents/MacOS/CodeFusion --help

To be able to type just codefusion, add an alias to your shell configuration once:

echo 'alias codefusion="/Applications/CodeFusion.app/Contents/MacOS/CodeFusion"' >> ~/.zshrc
source ~/.zshrc

Settings (parameters.json) on macOS

parameters.json is inside the app as well: /Applications/CodeFusion.app/Contents/MacOS/parameters.json. To edit it, run:
open -e /Applications/CodeFusion.app/Contents/MacOS/parameters.json

The help button next to the folder name in the Web UI also shows this location.

Updating on macOS

Replace the old CodeFusion.app with the new one and run the xattr -cr command (step 3) again. The new version comes with its own default parameters.json, because settings of an older version may not be compatible with the new one. If you changed parameters.json and would like to keep a copy, copy it somewhere else before replacing the app.

Docker Image

CodeFusion is also available as a Docker image. See the Docker documentation for detailed instructions on running CodeFusion in Docker.

Using the Tool

User Guide provides more information on how to use the tool in different mode (Graphical User Interface vs command line) as well as many configuration options